a program to format multiple sequence alignments in PostScript for publication and to assist in analysis. Alscript does not support point-and-click, but has a scripting language to allow complex effects.

a program for analysis of SAXS data that enables creation of 1D scattering profiles from 2D detector images, standard data operations such as averaging and subtraction, analysis of radius of gyration (Rg) and molecular weight, and advanced processing using GNOM, DAMMIF, and AMBIMETER. It also allows easy processing of inline SEC-SAXS data.

a computational pipeline for finding mutations relative to a reference sequence in short-read DNA re-sequencing data for microbial sized genomes. It reports single-nucleotide mutations, point insertions and deletions, large deletions, and new junctions supported by mosaic reads.

(Collaborative Computational Project for Electron cryo-Microscopy) a software framework and resulting software suite that includes tools for project and data management along with a focus on building and refinement of atomic models into cryo-EM reconstructions. The framework allows easy access to various programs and utilities from collaborators via Python task wrappers and a user-friendly graphical user interface or a command-line interface suitable for scripting.

a highly extensible, interactive molecular graphics program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. It is often a tool of choice for rendering EM volumes.

a novel automated particle picking software based on the deep learning object detection system 'You Only Look Once' (YOLO).
CrYOLO is available as standalone program under http://sphire.mpg.de/ and will be part of the image processing workflow in SPHIRE.

an optimising static compiler for both the Python programming language and the extended Cython programming language (based on Pyrex). It makes writing C extensions for Python as easy as Python itself.
cython is installed as a module within python.

an image processing package. It can be described as a distribution of ImageJ (and ImageJ2) together with Java, Java 3D and a lot of plugins organized into a coherent menu structure. Fiji compares to ImageJ as Ubuntu compares to Linux.

a popular way to view DNA sequence traces on Linux, Mac OSX, Windows, and Solaris. FinchTV started as the only chromatogram viewer that can display an entire trace in a scalable multi-pane view. And it leads the way with raw data views, BLAST searching and the ability to reverse complement sequences and traces.

converts both a 3D density map and an atom model into GMM (gaussian mixture model) by employing an EM (expectation maximization) algorithm. The program also has many other useful functions to handle GMM.

superimposes molecular subunits into the density map of their complex. To reduce computational costs for the superimposing, both subunits and complexes are transformed into GMM (Gaussian Mixture Model) using the gmconvert program. Although designed to superimpose multiple atomic models of subunits into a low-resolution 3D density map, gmfit can also be applied to superimposing two 3D density maps or two atomic models.

a portable command-line driven graphing utility originally created to allow scientists and students to visualize mathematical functions and data interactively. It has grown to support many non-interactive uses such as web scripting. It is also used as a plotting engine by third-party applications like CCP4.

provides a architecture for interactive computing with a browser-based notebook where you can combine code, text, mathematical expressions, inline plots, and other rich media into a single document and support for interactive data visualization. IPython is now part of the larger Jupyter project. Please see the [Jupyter website](http://jupyter.org/index.html) for more information.

the next-generation web-based user interface for Project Jupyter. JupyterLab enables you to work with documents and activities such as Jupyter notebooks, text editors, terminals, and custom components in a flexible, integrated, and extensible manner.

a system designed for automated collection of images from a transmission electron microscope; it includes the python-side programs written in python and c, the MySQL database and server, and the mainly php-based image and data viewers on a web server.

a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <200 sequences), FFT-NS-2 (fast; for alignment of <30,000 sequences).

an object-oriented Python library to analyze trajectories from molecular dynamics (MD) simulations in many popular formats. It can write most of these formats, too, together with atom selections suitable for visualization or native analysis tools.

(Minimal Ensemble Search) a genetic algorithm used to identify the minimal ensemble required to best ï¬t experimental data. The simulations provide an ensemble of molecular models from which a SAXS curve is calculated and compared to the experimental curve. Written by Martin Pelikan and Michal Hammel at Lawrence Berkeley Laboratory.

(Mixture-of-Isoforms) for isoform quantitation using RNA-Seq is a probabilistic framework that quantitates the expression level of alternatively spliced genes from RNA-Seq data, and identifies differentially regulated isoforms or exons across samples.
MISO is installed as a standalone program and as a module within python.

a simple command-line program that allows you to submit a single file of FASTA sequences over an internet connection to the NCBI BLAST databases. Searches are submitted through the client to the NCBI servers and do not need to download the databases locally (also called netblast and blastcl3).

an open source Message Passing Interface implementation that is developed and maintained by a consortium of academic, research, and industry partners. Open MPI is therefore able to combine the expertise, technologies, and resources from all across the High Performance Computing community in order to build the best MPI library available.

(Particle Estimation for Electron Tomography) a package for aligning and averaging particles in 3-D subvolumes extracted from tomograms. If PEET and IMOD are both installed, most PEET operations are available from the eTomo graphical user interface in IMOD. PEET is written in Matlab and a compiled version is distributed along with the Matlab runtime environment needed to run it.

(Protein-Ligand Interaction Profiler) for automated detection and visualization of relevant non-covalent protein-ligand contacts in 3D structures. Available as a stand alone application or a web service.

a multipurpose X11 plotting program that specializes in contour plots but can also handle 2D and 3D plots. The plot-types supported are: contour plots (rectangular grid, as well as triangular mesh), 2D line and scatter plots (x-vs-y), 3D surface , line and scatter plots, vector plots, probability plots, histograms, barcharts.

a GNU package containing software for programmers and technical users. Its centerpiece is libplot, a powerful C/C++ function library for exporting 2-D vector graphics in many file formats, both vector and raster. It can also do vector graphics animations. plotutils also contains command-line programs for plotting scientific data, many of which use libplot to export graphics.

(Persistence of Vision Raytracer) a high-quality, totally free tool for creating stunning three-dimensional graphics. It is available in official versions for Windows, Mac OS/Mac OS X and i86 Linux. The source code is available for those wanting to do their own ports. POVRAY was originally written by David Kirk Buck and Aaron A. Collins.

includes programs and shell scripts for electron tomography of thin specimens, providing an interactive graphical tool for fast initial alignment of a tilt series, shell scripts for the more time consuming refinement, and some other useful image manipulation utilities.

a general-purpose, interpreted, object oriented, high-level dynamic programming language that emphasizes code readability. Its syntax allows programmers to express concepts in fewer lines of code than in C++ or Java, thus allowing programmers to work more quickly and integrate their systems more effectively.

unifies standard tomogram processing steps in a single python-based toolbox. For subtomogram averaging, we implemented an adaptive adjustment of scoring and sampling that clearly improves the resolution of averages compared to static strategies.

cross platform time zone library that brings the Olson tz database into Python and allows accurate and cross platform timezone calculations using Python 2.4 or higher. It also solves the issue of ambiguous times at the end of daylight saving time, which you can read more about in the Python Library Reference (datetime.tzinfo).

a cross-platform application framework that is used for developing application software that can be run on various software and hardware platforms with little or no change in the underlying codebase, while still being a native application with native capabilities and speed.

an integrated development environment (IDE) for R that includes a console, syntax-highlighting editor that supports direct code execution, as well as tools for plotting, history, debugging and workspace management.

the program suite SASSIE (tools used to create atomistic models of molecular systems and to compare scattering data from these models directly to experimental data) plus “courtesy modules,” which include the molecular dynamics package NAMD, the scattering calculators Cryson and Crysol, and the program Hydropro for calculating hydrodynamic properties.

Restriction: available to nonprofit users who register with EMBL and send confirmation to SBGrid.

a plotting facility for SAXS-data, as well as a convenient tool to quickly generate plots for publication. Saxsview shows 1D-data in .dat, .int, .fit and .fir formats of the ATSAS package, the cansas .xml format (v1.0), as well as .csv files.

a graphical installation client used to install the SBGrid software collection on Apple OSX computers running MacOSX v10.9 - 10.12. Users can cherrypick a subset of applications for installation on their laptops or desktops. Software updates are highlighted, but users trigger the software update manually at their convenience.

a JAVA-based application for basic analysis of SAXS datasets. Scatter is developed by Robert Rambo at the Diamond Light Source (Didcot, UK). The program was previously developed at the SIBYLS beamline (12.3.1) of the Advanced Light Source, Berkeley, CA.

(pronounced “Sigh Pie”) a Python-based ecosystem of open-source software for mathematics, science, and engineering. In particular, these are some of the core packages: NumPy, SciPy Library, Matplotlib, IPython, Sympy, pandas

(Sequence Search and Alignment by Hashing Algorithm) a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences.
SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package.

(STructural Alignment of Multiple Proteins) a suite of programs to compare and align protein 3-D structures. It will multiply align structures and produce a corresponding sequence alignment with confidence values associated with each aligned position. It will also search a database of protein structures to identify structurally similar proteins and includes a number of utility programs for the manipulation of protein structures.

a pipeline that uses data obtained from ShapeMapper to model RNA secondary structures, including pseudoknots; identify de novo regions with well-defined and stable structures; and visualize most probable and alternative helices.

(Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. Tk is a graphical user interface toolkit that takes developing desktop applications to a higher level than conventional approaches.

a multiple sequence alignment package that can be used to align sequences or to combine the output of your favorite alignment methods (Clustal, Mafft, Probcons, Muscle...) into one unique alignment (M-Coffee).

a graphical front end to the diff program. It provides a side-by-side view of the differences between two files, along with several innovative features such as diff bookmarks and a graphical map of differences for quick navigation.

programs for cryo-tomography tilt-series alignment and subsequent tomographic reconstruction that take into consideration beam-induced sample motion, modeled by means of polynomial surfaces. TomoAlign comprises: 1) tomoalign, for alignment, to determine the basic parameters of the images (rotation, magnification, tilt) along with the polynomial coefficients that model the motion; 2) tomorec to calculate the tomogram from the tilt-series and takes into account the motion estimated ...

a comprehensive data analysis software package for hydrodynamic data from analytical ultracentrifugation experiments. It is the latest multi-platform version of UltraScan, which replaced the UltraScan II distribution. UltraScan II development has stopped although it is still available.

performs automated NMR data analysis for protein 3D structure determination. UNIO represents the result of more than a decade of innovative research performed in order to enable accurate, objective and highly automated protein structure determination by NMR.

a two-dimensional molecule drawing program for Unix operating systems that can read and write MDL Molfiles, and read ChemDraw text and binary files, to allow sharing between XDrawChem and other chemistry applications, and it can create images in popular formats like PNG and EPS.

an interactive image manipulation program for the X Window System that operates on images in the GIF, JPEG, TIFF, PBM, PGM, PPM, XPM, X11 bitmap, Sun Rasterfile, Targa, RLE, RGB, BMP, PCX, FITS, and PM formats on all known types of X displays. It can generate PostScript files, and (with ghostscript version 2.6 or above) it can also display them.